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  <ul>
<li class="navelem"><b>claragenomics</b></li><li class="navelem"><b>io</b></li><li class="navelem"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">FastaParser</a></li>  </ul>
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  <div class="summary">
<a href="#pub-methods">Public Member Functions</a> &#124;
<a href="classclaragenomics_1_1io_1_1FastaParser-members.html">List of all members</a>  </div>
  <div class="headertitle">
<div class="title">claragenomics::io::FastaParser Class Reference<span class="mlabels"><span class="mlabel">abstract</span></span></div>  </div>
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<div class="contents">

<p><code>#include &lt;<a class="el" href="fasta__parser_8hpp_source.html">fasta_parser.hpp</a>&gt;</code></p>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
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virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a213af5341107ea254176add6dd1dfd2d">~FastaParser</a> ()=default</td></tr>
<tr class="memdesc:a213af5341107ea254176add6dd1dfd2d"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html">FastaParser</a> implementations can have custom destructors, so delcare the abstract dtor as default. <br /></td></tr>
<tr class="separator:a213af5341107ea254176add6dd1dfd2d"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a04f6deee5108374fa485487e06e759e5"><td class="memItemLeft" align="right" valign="top">virtual int32_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a04f6deee5108374fa485487e06e759e5">get_num_seqences</a> () const =0</td></tr>
<tr class="memdesc:a04f6deee5108374fa485487e06e759e5"><td class="mdescLeft">&#160;</td><td class="mdescRight">Return number of sequences in FASTA file.  <a href="classclaragenomics_1_1io_1_1FastaParser.html#a04f6deee5108374fa485487e06e759e5">More...</a><br /></td></tr>
<tr class="separator:a04f6deee5108374fa485487e06e759e5"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a04a44819b81a93711295198492cc3765"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html">FastaSequence</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#a04a44819b81a93711295198492cc3765">get_sequence_by_id</a> (int32_t id) const =0</td></tr>
<tr class="memdesc:a04a44819b81a93711295198492cc3765"><td class="mdescLeft">&#160;</td><td class="mdescRight">Fetch an entry from the FASTA file by index position in file.  <a href="classclaragenomics_1_1io_1_1FastaParser.html#a04a44819b81a93711295198492cc3765">More...</a><br /></td></tr>
<tr class="separator:a04a44819b81a93711295198492cc3765"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ad37d794106d347d1d360d62db2d31cda"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html">FastaSequence</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1io_1_1FastaParser.html#ad37d794106d347d1d360d62db2d31cda">get_sequence_by_name</a> (const std::string &amp;name) const =0</td></tr>
<tr class="memdesc:ad37d794106d347d1d360d62db2d31cda"><td class="mdescLeft">&#160;</td><td class="mdescRight">Fetch an entry from the FASTA file by name.  <a href="classclaragenomics_1_1io_1_1FastaParser.html#ad37d794106d347d1d360d62db2d31cda">More...</a><br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>FASTA file parser </p>
</div><h2 class="groupheader">Member Function Documentation</h2>
<a id="a04f6deee5108374fa485487e06e759e5"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a04f6deee5108374fa485487e06e759e5">&#9670;&nbsp;</a></span>get_num_seqences()</h2>

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          <td class="memname">virtual int32_t claragenomics::io::FastaParser::get_num_seqences </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
        </tr>
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<p>Return number of sequences in FASTA file. </p>
<dl class="section return"><dt>Returns</dt><dd>Sequence count in file </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#a04a44819b81a93711295198492cc3765">&#9670;&nbsp;</a></span>get_sequence_by_id()</h2>

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          <td class="memname">virtual <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html">FastaSequence</a> claragenomics::io::FastaParser::get_sequence_by_id </td>
          <td>(</td>
          <td class="paramtype">int32_t&#160;</td>
          <td class="paramname"><em>id</em></td><td>)</td>
          <td> const</td>
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<p>Fetch an entry from the FASTA file by index position in file. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">id</td><td>Position of sequence in file. If id is greater than file size, an error is thrown.</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html" title="A structure to hold details of a single FASTA entry.">FastaSequence</a> object describing the entry. </dd></dl>

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<h2 class="memtitle"><span class="permalink"><a href="#ad37d794106d347d1d360d62db2d31cda">&#9670;&nbsp;</a></span>get_sequence_by_name()</h2>

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          <td class="memname">virtual <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html">FastaSequence</a> claragenomics::io::FastaParser::get_sequence_by_name </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>name</em></td><td>)</td>
          <td> const</td>
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<p>Fetch an entry from the FASTA file by name. </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">name</td><td>Name of the sequence in FASTA file. If there is no entry by that name, an error is thrown.</td></tr>
  </table>
  </dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>A <a class="el" href="structclaragenomics_1_1io_1_1FastaSequence.html" title="A structure to hold details of a single FASTA entry.">FastaSequence</a> object describing the entry. </dd></dl>

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<hr/>The documentation for this class was generated from the following file:<ul>
<li>common/io/include/claragenomics/io/<a class="el" href="fasta__parser_8hpp_source.html">fasta_parser.hpp</a></li>
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